Breeding high-photosynthetic-efficiency wheat varieties is a crucial link in safeguarding national food security. Traditional identification methods necessitate laborious on-site observation and measurement, consuming time and effort. Leveraging unmanned aerial vehicle (UAV) remote sensing technology to forecast photosynthetic indices opens up the potential for swiftly discerning high-photosynthetic-efficiency wheat varieties. The objective of this research is to develop a multi-stage predictive model encompassing nine photosynthetic indicators at the field scale for wheat breeding. These indices include soil and plant analyzer development (SPAD), leaf area index (LAI), net photosynthetic rate (Pn), transpiration rate (Tr), intercellular CO2 concentration (Ci), stomatal conductance (Gsw), photochemical quantum efficiency (PhiPS2), PSII reaction center excitation energy capture efficiency (Fv’/Fm’), and photochemical quenching coefficient (qP). The ultimate goal is to differentiate high-photosynthetic-efficiency wheat varieties through model-based predictions. This research gathered red, green, and blue spectrum (RGB) and multispectral (MS) images of eleven wheat varieties at the stages of jointing, heading, flowering, and filling. Vegetation indices (VIs) and texture features (TFs) were extracted as input variables. Three machine learning regression models (Support Vector Machine Regression (SVR), Random Forest (RF), and BP Neural Network (BPNN)) were employed to construct predictive models for nine photosynthetic indices across multiple growth stages. Furthermore, the research conducted principal component analysis (PCA) and membership function analysis on the predicted values of the optimal models for each indicator, established a comprehensive evaluation index for high photosynthetic efficiency, and employed cluster analysis to screen the test materials. The cluster analysis categorized the eleven varieties into three groups, with SH06144 and Yannong 188 demonstrating higher photosynthetic efficiency. The moderately efficient group comprises Liangxing 19, SH05604, SH06085, Chaomai 777, SH05292, Jimai 22, and Guigu 820, totaling seven varieties. Xinmai 916 and Jinong 114 fall into the category of lower photosynthetic efficiency, aligning closely with the results of the clustering analysis based on actual measurements. The findings suggest that employing UAV-based multi-source remote sensing technology to identify wheat varieties with high photosynthetic efficiency is feasible. The study results provide a theoretical basis for winter wheat phenotypic monitoring at the breeding field scale using UAV-based multi-source remote sensing, offering valuable insights for the advancement of smart breeding practices for high-photosynthetic-efficiency wheat varieties.